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- EMDB-1285: Structure of the ribosome-bound cricket paralysis virus IRES RNA. -

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Basic information

Entry
Database: EMDB / ID: 1285
TitleStructure of the ribosome-bound cricket paralysis virus IRES RNA.
Sampleyeast 80S ribosome in complex with the CrPV IRES RNA
SourceSaccharomyces cerevisiae / yeast / Baker's Yeast, Baker / サッカロミセス・セレビシエ /
Map dataComplex between the yeast 80S ribosome and the cricket paralysis virus IRES
Methodsingle particle reconstruction, at 7.3 Å resolution
AuthorsSchuler M / Connell SR / Lescoute A / Giesebrecht J / Dabrowski M / Schroeer B / Mielke T / Penczek PA / Westhof E / Spahn CM
CitationNat. Struct. Mol. Biol., 2006, 13, 1092-1096

Nat. Struct. Mol. Biol., 2006, 13, 1092-1096 StrPapers
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn

DateDeposition: Oct 31, 2006 / Header (metadata) release: Oct 31, 2006 / Map release: Oct 31, 2007 / Last update: Oct 31, 2006

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 1.2
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-2noq
  • Surface level: 1.2
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-2noq
  • Imaged by Jmol
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Supplemental images

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Map

Fileemd_1285.map.gz (map file in CCP4 format, 105470 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.22 Å/pix.
= 366. Å
300 pix
1.22 Å/pix.
= 366. Å
300 pix
1.22 Å/pix.
= 366. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.22 Å
Density
Contour Level:2.76, 1.2 (movie #1):
Minimum - Maximum-6.03604 - 12.0446
Average (Standard dev.)0.0102696 (1.28183)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 366 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.221.221.22
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z366.000366.000366.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-6.03612.0450.010

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Supplemental data

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Sample components

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Entire yeast 80S ribosome in complex with the CrPV IRES RNA

EntireName: yeast 80S ribosome in complex with the CrPV IRES RNA / Number of components: 2

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Component #1: ribosome-eukaryote, yeast 80S ribosome

Ribosome-eukaryoteName: yeast 80S ribosome / Eukaryote: ALL / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /

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Component #2: nucleic-acid, CrPV IRES

Nucleic-acidName: CrPV IRES / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3900 nm
Specimen HolderHolder: Eucentric / Model: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 341 / Scanner: PRIMESCAN / Sampling size: 4.7 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 73313 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: projection matching / Software: SPIDER / CTF correction: Defocus groups / Resolution: 7.3 Å / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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